How to keep logic bricks organized?
Organizing with states

You can use the states of the build-in state machine to group your bricks. 

This allows to quickly show/hide/switch logical groups. You can do that by selecting/deselecting states in the visible-state-bar. 

Requirements

Make sure all states with logic are enabled in the initial-state-bar.

Example

This way you can group this logic:


into movement logic:


using logic by keyboard



and using logic by mouse



Hints


You do not need to use the state machine operations (state
switching).  
You can select multiple states at the same time by
holding  when selecting/deselecting a state.
If you need more than the 30 available states I think it is time to review your design. Most-likely this object simply does too much. It would be better to spread the logic over multiple objects.